<html>
<body style="padding:20px;width:650px;">
<title>Cluster Table</title>
<h2>Cluster Table</h2>


<ul> 
<li>Columns can be added/removed using the <b>Select Columns</b> button below the table. 
<li>Columns can
also be rearranged (by dragging the headers) and sorted (by clicking the headers). 
<li>Put the mouse over a column name in the <b>Select Columns</b> interface, and a full explanation of the column is shown
in the lower left corner.
<li>One or more cluster rows can be selected using mouse click, shift-click, or ctrl-click.
</ul>
<h3>Functions at the top:</h3>
<table border=0 cellspacing=3>
<tr><td valign="top"><i>View Selected Clusters</i><td> Select a cluster or clusters followed by this function to view the members.
<tr><td valign="top"><i>Clear</i><td> Clears the table of selections.
<tr><td valign="top"><i>Export</i><td> Exports the table to file.
<tr><td valign="top"><i>Copy</i><td> Copies to the clipboard either the entire table, 
or the ClusterID of the selected row (if exactly one row is selected). A menu is provided with the choice.
</table>

<h3>Cluster Columns:</h3>
<p>
<i>General</i>
<table border=0 cellspacing=3>
<tr><td valign="top">&nbsp;&nbsp;&nbsp;ClusterID <td>Unique id of the cluster formed as &lt;method prefix&gt;_&lt;number&gt;
<tr><td>&nbsp;&nbsp;&nbsp;Count<td>Number of sequences in the cluster
<tr><td  valign="top">&nbsp;&nbsp;&nbsp;Taxa<td> Notation "nxN" where n is the number of distinct species included in the cluster,
where N=1 if all the species are represented by single sequences and N="N" if any of the
species have more than 1 member in the cluster.
<tr><td  valign="top">&nbsp;&nbsp;&nbsp;Method<td> Name of the clustering method; note, more than one clustering set
may have been entered into the database, where they each have a unique name. 
</table>

<p>
<i>Majority Hit</i>
<br>
The majority hit is the annotation
shared by the majority of individual sequences, over all their hits (i.e. not just their
best hits; see Members Help for more information on hits). 
<br>The 'Percent' with the hit uses the majority description. The hitID and associated information 
uses the majority ID with that description.
<br><i>This is only to give an idea of the
function of the cluster, but the cluster should be inspected to understand the variety
of functions assigned.</i>
<table border=0 cellspacing=3>
<tr><td valign="top">&nbsp;&nbsp;&nbsp;ID<td> The identifier from the database, e.g. the UniProt ID.
<tr><td valign="top">&nbsp;&nbsp;&nbsp;Eval<td> The best BLAST e-value from all the sequences in the cluster that have this
hit.
<tr><td valign="top">&nbsp;&nbsp;&nbsp;Percent<td> The percentage of sequences in the cluster that have this hit.
<tr><td valign="top">&nbsp;&nbsp;&nbsp;Descript<td> The hit description.
<tr><td valign="top">&nbsp;&nbsp;&nbsp;Species<td> The hit species.
<tr><td valign="top">&nbsp;&nbsp;&nbsp;Type<td> Type of database (i.e. sp for SwissProt and tr for TrEMBL). 
<tr><td valign="top">&nbsp;&nbsp;&nbsp;Tag<td> The tag assigned (e.g. the taxonomy such as 'plants'). 
<tr><td valign="top">&nbsp;&nbsp;&nbsp;Len<td> Length of protein.
</table>
The last 5 values are taken from the first singleTCW that contains the protein as a hit.


<p>
<i>Percent pairs with PCC>=0.8</i>
<br>
For each cluster, for each pair, the Pearson's Correlation Coefficient is computed from the
RPKM values of the libraries shared between the two sequences, where libraries are 'shared' if
they have the same name. There are two columns for this:
<table border=0 cellspacing=3>
<tr><td valign="top">&nbsp;&nbsp;&nbsp;perPCC<td> The percent of pairs that have PCC>=0.8. For example, if a cluster has 4 sequences,
it has (4*3)/2 = 6 pairs. If two of them have PCC>=0.8, then the perPCC will be 33%. A perPCC of
100% means that their expression profiles on their shared libraries are highly correlated.
<tr><td valign="top">&nbsp;&nbsp;&nbsp;maxPCC<td> The maximum PCC value from all pairs.
</table>
To view what pairs have PCC>=0.8, select the cluster and then select sequences with in the cluster.
The "View Detail" lists members with which the selected sequence has a PCC>=0.8. 

<p>
<i>Percent sequences with PRKM>=1000.0</i>
<br>This provides evidence of what clusters are highly expressed.


<p>
<i>DataSet Counts</i>
<br>
If checked, then a column shows the count of sequences coming from that species.

<p>
<i>Percent sequences with DE<=0.05</i>

